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DEScan2 (development version)

DEScan2

This is the development version of DEScan2; for the stable release version, see DEScan2.

Differential Enrichment Scan 2

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DOI: 10.18129/B9.bioc.DEScan2

Bioconductor version: Development (3.23)

Integrated peak and differential caller, specifically designed for broad epigenomic signals.

Author: Dario Righelli [aut, cre], John Koberstein [aut], Bruce Gomes [aut], Nancy Zhang [aut], Claudia Angelini [aut], Lucia Peixoto [aut], Davide Risso [aut]

Maintainer: Dario Righelli <dario.righelli at gmail.com>

Citation (from within R, enter citation("DEScan2")):

Installation

To install this package, start R (version "4.6") and enter:


if (!require("BiocManager", quietly = TRUE))
 install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
BiocManager::install("DEScan2")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("DEScan2")

DEScan2 Vignette HTML R Script

Reference Manual PDF

NEWS Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews Coverage, Epigenetics, ImmunoOncology, PeakDetection, Sequencing, Software

Version 1.31.0

In Bioconductor since BioC 3.7 (R-3.5) (7.5 years)

License Artistic-2.0

Depends R (>= 3.5), GenomicRanges

Imports BiocParallel, BiocGenerics, ChIPpeakAnno, data.table, DelayedArray, Seqinfo, GenomeInfoDb, GenomicAlignments, glue, IRanges, plyr, Rcpp (>= 0.12.13), rtracklayer, S4Vectors(>= 0.23.19), SummarizedExperiment, tools, utils

System Requirements

URL

See More

Suggests BiocStyle, knitr, rmarkdown, testthat, edgeR, limma, EDASeq, RUVSeq, RColorBrewer, statmod

Linking To Rcpp, RcppArmadillo

Enhances

Depends On Me

Imports Me

Suggests Me

Links To Me

Build Report Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package DEScan2_1.31.0.tar.gz

Windows Binary (x86_64)

macOS Binary (x86_64)

macOS Binary (arm64)

Source Repository git clone https://git.bioconductor.org/packages/DEScan2

Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/DEScan2

Bioc Package Browser https://code.bioconductor.org/browse/DEScan2/

Package Short Url https://bioconductor.org/packages/DEScan2/

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